CoPilot only runs when Travis CI runs. So if you've enabled your repository in Travis, you could make a "copilot" branch off of master, check in the CoPilot configuration there, and Travis should only build that branch. When Travis builds it, CoPilot will scan it, and you should get results only for your "copilot" branch.

Let me know if you need any more help, and thanks for your interest in CoPilot!